Talk:Codon usage bias

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Comment

It should start with a definition for codon usage bias, with the words in boldface. I can't see why this isn't possible. Richard001 (talk) 08:29, 14 August 2008 (UTC)[reply]

The codons are redundant and degenerate. This is because each unique codon, encodes a SINGLE amino acid; but most of the 20 amino acids are coded for by more than one codon. Enzymes-GMU (talk) 17:20, 18 September 2009 (UTC)[reply]

There is no mention here of histone wrapping as another factor in codon selection. — Preceding unsigned comment added by 2601:242:C201:7890:D13D:D071:2DCC:9F77 (talk) 05:15, 23 January 2017 (UTC)[reply]

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extraneous logo

There was a sequence logo from a methods paper by Dutihl, et al https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3129529/ that is completely extraneous to this article. The logo condenses a lot of amino acid profiles from an automated gene-identification system. It has nothing to do with codon usage bias. Dabs (talk) 18:07, 29 August 2019 (UTC)[reply]

Updates needed to theory section

This article does not mention biased gene conversion anywhere. The theory section does not reflect the literature from the past 15 years. The mutation-selection-drift model ^[1] was a prevailing view until the late 1990s when evidence for biased gene conversion began to accumulate. Dabs (talk) 18:38, 29 August 2019 (UTC)[reply]

Suggested revision

begin with Bulmer's mut-sel-drift model as a baseline. this allows both mutational and selective effects. Shah and Gilchrist ^[2] as exemplar
explain how Hershberg and Petrov ^[3] undermined the mutationist hypothesis for genome composition by showing that mutation is generally AT-biased
introduce the idea of biased gene conversion via key source ^[4] and more recent sources such as ^[5] and ^[6]
restate synopsis of current thinking on causes (should also appear earlier in this article), and explain some of the taxonomically variable factors important in these models. Fold in the content of "contributing factors" section which can be deleted.
- population size
- diploidy and sex
- tRNA repertoire

Some sources

Galtier N, Roux C, Rousselle M, Romiguier J, Figuet E, Glémin S, Bierne N,

Duret L. Codon Usage Bias in Animals: Disentangling the Effects of Natural Selection, Effective Population Size, and GC-Biased Gene Conversion. Mol Biol Evol. 2018 May 1;35(5):1092-1103. doi: 10.1093/molbev/msy015. PubMed PMID: 29390090.

Rousselle M, Laverré A, Figuet E, Nabholz B, Galtier N. Influence of

Recombination and GC-biased Gene Conversion on the Adaptive and Nonadaptive Substitution Rate in Mammals versus Birds. Mol Biol Evol. 2019 Mar 1;36(3):458-471. doi: 10.1093/molbev/msy243. PubMed PMID: 30590692; PubMed Central PMCID: PMC6389324.

Behura SK, Severson DW. Codon usage bias: causative factors, quantification

methods and genome-wide patterns: with emphasis on insect genomes. Biol Rev Camb Philos Soc. 2013 Feb;88(1):49-61. doi: 10.1111/j.1469-185X.2012.00242.x. Epub 2012 Aug 14. Review. PubMed PMID: 22889422.

Kaiser CM, Liu K. Folding up and Moving on-Nascent Protein Folding on the

Ribosome. J Mol Biol. 2018 Oct 26;430(22):4580-4591. doi: 10.1016/j.jmb.2018.06.050. Epub 2018 Jul 5. Review. PubMed PMID: 29981746; PubMed Central PMCID: PMC6384192.

References

^ M. Bulmer (1991). "The selection-mutation-drift theory of synonymous codon usage". Genetics. 129: 897–907.
^ P. Shah and M. A. Gilchrist (2011). "Explaining complex codon usage patterns with selection for translational efficiency, mutation bias, and genetic drift". Proceedings of the National Academy of Sciences of the United States of America. 108: 10231–6. doi:10.1073/pnas.1016719108.
^ R. Hershberg and D. A. Petrov (2010). "Evidence that mutation is universally biased towards AT in bacteria". PLoS Genet. 6: e1001115. doi:10.1371/journal.pgen.1001115.{{cite journal}}: CS1 maint: unflagged free DOI (link)
^ L. Duret and N. Galtier (2009). "Biased gene conversion and the evolution of mammalian genomic landscapes". Annu Rev Genomics Hum Genet. 10: 285–311. doi:10.1146/annurev-genom-082908-150001.
^ N. Galtier, C. Roux, M. Rousselle, J. Romiguier, E. Figuet, S. Glemin, N. Bierne and L. Duret (2018). "Codon Usage Bias in Animals: Disentangling the Effects of Natural Selection, Effective Population Size, and GC-Biased Gene Conversion". Mol Biol Evol. 35: 1092–1103. doi:10.1093/molbev/msy015.{{cite journal}}: CS1 maint: multiple names: authors list (link)
^ M. Rousselle, A. Laverre, E. Figuet, B. Nabholz and N. Galtier (2019). "Influence of Recombination and GC-biased Gene Conversion on the Adaptive and Nonadaptive Substitution Rate in Mammals versus Birds". Mol Biol Evol. 36: 458–471. doi:10.1093/molbev/msy243.{{cite journal}}: CS1 maint: multiple names: authors list (link)

[Bulmer1991-1] M. Bulmer (1991). "The selection-mutation-drift theory of synonymous codon usage". Genetics. 129: 897–907.

[ShahGilchrist2011-2] P. Shah and M. A. Gilchrist (2011). "Explaining complex codon usage patterns with selection for translational efficiency, mutation bias, and genetic drift". Proceedings of the National Academy of Sciences of the United States of America. 108: 10231–6. doi:10.1073/pnas.1016719108.

[HershbergPetrov2010-3] R. Hershberg and D. A. Petrov (2010). "Evidence that mutation is universally biased towards AT in bacteria". PLoS Genet. 6: e1001115. doi:10.1371/journal.pgen.1001115.{{cite journal}}: CS1 maint: unflagged free DOI (link)

[DuretGaltier2009-4] L. Duret and N. Galtier (2009). "Biased gene conversion and the evolution of mammalian genomic landscapes". Annu Rev Genomics Hum Genet. 10: 285–311. doi:10.1146/annurev-genom-082908-150001.

[Galtier2018-5] N. Galtier, C. Roux, M. Rousselle, J. Romiguier, E. Figuet, S. Glemin, N. Bierne and L. Duret (2018). "Codon Usage Bias in Animals: Disentangling the Effects of Natural Selection, Effective Population Size, and GC-Biased Gene Conversion". Mol Biol Evol. 35: 1092–1103. doi:10.1093/molbev/msy015.{{cite journal}}: CS1 maint: multiple names: authors list (link)

[Rousselle2019-6] M. Rousselle, A. Laverre, E. Figuet, B. Nabholz and N. Galtier (2019). "Influence of Recombination and GC-biased Gene Conversion on the Adaptive and Nonadaptive Substitution Rate in Mammals versus Birds". Mol Biol Evol. 36: 458–471. doi:10.1093/molbev/msy243.{{cite journal}}: CS1 maint: multiple names: authors list (link)

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